HEADER DNA 14-MAR-94 170D TITLE SOLUTION STRUCTURE OF A DNA DODECAMER CONTAINING THE ANTI-NEOPLASTIC TITLE 2 AGENT ARABINOSYLCYTOSINE: COMBINED USE OF NMR, RESTRAINED MOLECULAR TITLE 3 DYNAMICS AND FULL RELAXATION MATRIX REFINEMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA/RNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*T)-R(P*CAR)- COMPND 3 D(P*GP*CP*G)-3'); COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED KEYWDS DNA EXPDTA SOLUTION NMR AUTHOR B.I.SCHWEITZER,T.MIKITA,G.W.KELLOGG,K.H.GARDNER,G.P.BEARDSLEY REVDAT 5 16-FEB-22 170D 1 REMARK LINK REVDAT 4 24-FEB-09 170D 1 VERSN REVDAT 3 01-APR-03 170D 1 JRNL REVDAT 2 15-JAN-95 170D 1 COMPND SEQRES REVDAT 1 31-JUL-94 170D 0 JRNL AUTH B.I.SCHWEITZER,T.MIKITA,G.W.KELLOGG,K.H.GARDNER, JRNL AUTH 2 G.P.BEARDSLEY JRNL TITL SOLUTION STRUCTURE OF A DNA DODECAMER CONTAINING THE JRNL TITL 2 ANTI-NEOPLASTIC AGENT ARABINOSYLCYTOSINE: COMBINED USE OF JRNL TITL 3 NMR, RESTRAINED MOLECULAR DYNAMICS, AND FULL RELAXATION JRNL TITL 4 MATRIX REFINEMENT. JRNL REF BIOCHEMISTRY V. 33 11460 1994 JRNL REFN ISSN 0006-2960 JRNL PMID 7918360 JRNL DOI 10.1021/BI00204A008 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES WERE GENERATED IN THE REMARK 3 FOLLOWING MANNER: RESTRAINED MOLECULAR DYNAMICS WAS PERFORMED REMARK 3 WITH EXPERIMENTAL DISTANCE AND DIHEDRAL RESTRAINTS GENERATED REMARK 3 FROM NOESY AND COSY NMR DATA. THREE STRUCTURES WERE GENERATED REMARK 3 STARTING FROM CANONICAL A-TYPE DNA AND THREE STRUCTURES STARTING REMARK 3 FROM CANONICAL B-TYPE DNA. FOR BOTH CONTROL AND ARAC STRUCTURES, REMARK 3 THE RMSD OF THE SIX STRUCTURES WAS < 0.7 ANGSTROM. THE SIX REMARK 3 STRUCTURES WERE AVERAGED, MINIMIZED AND REFINED USING RELAXATION REMARK 3 MATRIX REFINEMENT IN A DYNAMICAL SIMULATED ANNEALING PROTOCOL. REMARK 3 THE X-PLOR DISTANCE CONSTRAINT AND SUGAR DIHEDRAL CONSTRAINT REMARK 3 TABLES USED IN THE RESTRAINED MOLECULAR DYNAMICS CALCULATIONS REMARK 3 FOR THE ARAC-CONTAINING DODECAMER ARE AVAILABLE FROM THE PROTEIN REMARK 3 DATA BANK AS A SEPARATE ENTRY. REMARK 4 REMARK 4 170D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000170158. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : MOLECULAR DYNAMICS, MATRIX REMARK 210 RELAXATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 6 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 171D RELATED DB: PDB DBREF 170D A 1 12 PDB 170D 170D 1 12 DBREF 170D B 13 24 PDB 170D 170D 13 24 SEQRES 1 A 12 DC DG DC DG DA DA DT DT CAR DG DC DG SEQRES 1 B 12 DC DG DC DG DA DA DT DT CAR DG DC DG MODRES 170D CAR A 9 DC CYTOSINE ARABINOSE-5'-PHOSPHATE MODRES 170D CAR B 21 DC CYTOSINE ARABINOSE-5'-PHOSPHATE HET CAR A 9 31 HET CAR B 21 31 HETNAM CAR CYTOSINE ARABINOSE-5'-PHOSPHATE FORMUL 1 CAR 2(C9 H14 N3 O8 P) LINK O3' DT A 8 P CAR A 9 1555 1555 1.61 LINK O3' CAR A 9 P DG A 10 1555 1555 1.60 LINK O3' DT B 20 P CAR B 21 1555 1555 1.61 LINK O3' CAR B 21 P DG B 22 1555 1555 1.60 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000